I'm trying to loop in a cycle, output each value and then print the result of some other function.
But the output looks strange, the output of the loop mixed with the output of the other function.
Is there any way to synchronise it? I'm using Jupyter, not Julia console.
As Gnimuc K. pointed out in comments:
this has already been fixed here, but unreleased yet. you should work
on the master via Pkg.checkout("IJulia")
Related
I have just started to learn to code on R, so I apologize for the very simple question. I understand it is best to type your code in as a Script so you can edit and save it. However, when I try to make an object in the script section, it does not work. If I make an object in the console, R saves the object and it appears in my environment. I am typing in a very simple code to try a quick exercise on rolling dice:
die <- 1:6
But it only works in the console and not when typed as a script. Any help/explanation appreciated!
Essentially, you interact with R environment differently when running an .R script via RScript.exe or via console with R.exe, Rterm, etc. and in GUI IDEs like RGui or RStudio. (This applies to any programming language with interactive compilers not just R).
The script does save thedie object in R environment but only during the run or lifetime of that script (i.e., from beginning to end of code lines). Your code line is simply an assignment of object. You do nothing with it. Apply some function, output results, and other actions in that script to see.
On the console, the R environment persists interactively until you quit it with q(). So assigned objects remains for lifetime of your console session. After assigning, you can afterwards apply function, output results, or other actions in line by line calls.
Ultimately, scripts gathers all line by line code in advance of run for automated execution without relying on user to supply lines. Imagine running 1,000 lines of code with nested if/then or for/while loops, apply functions on console! Therefore, have all your R coding needs summarily handled in scripts.
It is always better to have the script, as you say, you can save edit correct, without having to rewrite the code to change a variable or number.
I recommend using Rstudio, it is very practical and will help you to program more efficiently and allows you to see, among other things, the different objects that you have created.
I tried using a for loop to print out a few rows. here is the code.
Weird thing is that it doesn't work for head() function. It works if I replaced head() with print().
kw_id=c('a','b')
keyword_text=data.frame(col=c('a','b'), col2=c(1,2), row.names=(c('r1','r2')))
for (i in 1:2) {
plot_data<-subset(keyword_text,col==kw_id[i])
print(plot_data)
head(plot_data)
}
Could someone help? I suspect it has something to do with head() function.
This is a relatively common class of problem that newcomers to R run into. The issue here is that R serves two mistresses: interactive console work and "true programming".
When you type a command at the console that returns a value, the console automatically calls a print method in order to display the results. When running a script, this doesn't happen unless you tell it to.
So if you changed it to print(head(plot_data)) it should work.
These are discussed in FAQ 7.16 and 7.22
Addendum lifted from the comments:
As Josh points out, copy+pasting the for loop directly to the console also fails to print any output. What's going on in that case is that for loops (like most everything in R) is actually a function, and it's return value (NULL) is returned invisibly, which means no printing. (This is mentioned in ?Control.)
Does R provide a similar command for debugging like Matlab's keyboard?
This command provides an interactive shell and can be used in any function.
This gives access to all variables allowing one to verify that the input data is really what it should be (or test why it's not working as expected).
Makes debugging a lot easier (at least in Matlab...).
It sounds like you're looking for browser().
From the description:
A call to ‘browser’ can be included in the body of a function.
When reached, this causes a pause in the execution of the current
expression and allows access to the R interpreter.
It sounds like you're new to debugging in R so you might want to read Hadley's wiki page on debugging.
Have a look at ?recover, this function provides great debugging functionality.
Is there something like the Common Lisp function DRIBBLE or Unix command tee in R?
Specifically, I want everything I type and everything R prints back to me to be appended to a file (tee only captures stdout; I want everyting: errors, warnings, print, cat, my input).
I found a 10 year old message on the subject which offers a weak version of that (it does not capture the output from cat/print).
The standard function sink only captures (not duplicates) the R's output; and it does not capture my input.
Is there a better way?
Look at the txtStart function (and related functions) in the TeachingDemos package. I think that it does everything you want except capturing errors (and the TaskCallback system in the R guts needs to be updated for that to happen).
The other option is to run R inside of another environment such as ESS (inside of Emacs) (there are others, but I am less familiar with them). Then everything is captured in the editor/buffer and can be saved to a file.
Note that the sink function does have a split argument that works like tee to show the output on screen as well as duplicate it to the file, but it still only does the output, not the input commands.
You probably want sink() -- see help(sink) for examples.
I've an R script, that takes commandline arguments, where the top line is:
#!/usr/bin/Rscript --slave
I wanted to interrupt execution in a function (so I can interactively use the data variables that have been loaded by that point to work out the next bit of code I need to write). I added this inside the function in question:
browser()
but it gets ignored. A bit of searching suggests it might be because the program is running in non-interactive mode. But even more searching has not tracked down how I switch the script out non-interactive mode so that browser() will work. Something like a browser_yes_I_really_mean_it() function.
P.S. I want to avoid altering the rest of the script if at all possible. My current approach is to copy and paste the code chunks, needed to prepare the data, into an interactive session; but as the script gets more and more complex this is getting more and more unreasonable.
UPDATE: for anyone else with the same question, it appears the answer to the actual question is that it is impossible. Once you start R in a non-interactive mode the die is cast. The given answers are therefore workarounds: either you hack your code (remembering to unhack it afterwards), or you refactor to make debugging easier. (This comment is not intended as a criticism of the answers; the suggested refactoring makes the code cleaner anyway.)
Can you just fire up R and source the file instead?
R
source("script.R")
Following mdsumner's answer, I edited my script like this:
if(!exists("argv")){
argv=commandArgs(TRUE)
if(length(argv)!=4)usage_and_exit()
}else{
if(length(argv)!=4){
stop("Must set argv as a 4 element vector. E.g. argv=c(...)")
}
}
Then no other change was needed, and I was able to do:
R
> argv=c('a','b','c','d')
> source("script.R")
In addition to the previous answer, I'd create a toplevel function (e.g. doStuff) which performs the analysis you want to perform in batch. The function takes the cmd line options as input. In the batch script you source the script that contains this function and call it. In this way you can easily run the function in interactive mode and use e.g. browser().
In some cases, the suggested solution (workaround) may not work - for example, when the R code needs to be run as a part of an existing bash script. For those cases, I suggest to write in your R script into the bash script using here document:
#!/bin/bash
R --interactive << EOT
# R code starts here
argv=c('a','b','c','d')
print(interactive())
# Rest of script contents
quit("no")
# R code ends here
EOT
This way, print(interactive()) above will yield TRUE.
Sidenote: Make sure to avoid the $ character in your R code, as this would not be processed correctly - for example, retrieve a column from a data.frame() by using df[["X1"]] instead of df$X1.